Seattle Cancer Consortium Breast SPORE

Seattle Cancer Consortium Breast SPORE

Principal Investigators: Peggy L. Porter, MD
Martin “Mac” Cheever, MD

Overall Program Description
The Seattle Cancer Consortium (SCC) Breast SPORE application, led by Drs. Peggy Porter and Martin
“Mac” Cheever, brings together clinical and laboratory researchers from the Fred Hutch and the University of Washington (UW) with a goal to positively impact breast cancer prevention, detection, treatment and care of women who have, or are at risk for, the disease. To achieve that goal, we will carry out strategic research in highly translational projects, develop new research directions as the SPORE progresses, and sponsor new investigators—those starting their careers and those with established careers newly focusing on breast cancer.

The investigators in this SPORE view the highly variable response of breast cancers to current therapies as a manifestation of the genotypic and phenotypic heterogeneity of the disease. Therefore, the initial projects on the SPORE will focus on the supposition that targeted treatments need to be focused on the appropriate tumor type. The four major research projects proposed for the Seattle SPORE expand on this theme. Two of the projects are initiated with clinical trials and a focused bed-side-to-bench translational approach. Three of the projects are focused on gaining insight into resistance to therapy and eventually defining what targeted therapies are needed to treat resistant tumors. Project 1 will apply basic discovery of p27kip1 cell cycle regulation in breast cancer to predict mortality and response to therapy. Project 2 will use exquisitely specific and engineered central memory T cells to target abnormally expressed tumor-associated proteins with vaccines and therapy. Project 3 will determine the biological basis for a breast imaging metabolism/perfusion mismatch profile that predicts poor prognosis and poor response to systemic therapy. Project 4, will draw on a well-characterized population-based cohort to identify specific DNA damage pathway biomarkers that could prevent the over, or under, treatment of women with breast cancer.

Together, these four projects afford both short- and long-term translational rewards and potential for new discoveries that will impact important aspects of breast cancer care. The SPORE is enhanced by a Developmental Research Program (DRP), a Career Development Program (CDP) and four supporting Cores: Leadership, Specimen Acquisition and Pathology, Clinical, and Biostatistics. These elements, along with the existing highly interactive and interdisciplinary environment and outstanding institutional support for breast cancer research in the FH/UW Cancer Consortium, ensure a successful translational SPORE program in breast cancer.

CDK2 activity is controlled by two primary mechanisms: CDK2 inhibitors such as p27, and inhibitory phosphorylation. Our studies of p27 in Aim 1 focus on the first mechanism, whereas this new direction seeks to target inhibitory phosphorylation. We are developing a new therapeutic approach that exploits a cell cycle control mechanism that relies upon CDK2 inhibitory phosphorylation, with the hope of to achieving durable responses of breast cancers by using minimally toxic chemotherapy that induces replication stress. This work builds upon our recent findings that CDK2 inhibitory phosphorylation is essential for normal cellular responses to replication stress, and that impaired CDK2 inhibitory phosphorylation during replication stress results in irreparable DNA damage and permanent cell cycle exit. Drugs that induce replication stress by inhibiting DNA synthesis induce a DNA damage response that is mediated by the S-phase checkpoint, and this requires CDK2 inhibitory phosphorylation. We intend to utilize CDK2-driven replication stress failure to convert drugs that induce transient replication stress into agents that permanently inhibit breast cancer cell proliferation. Mutations that deregulate CDKs and are among the most common genetic events in breast cancers, and our data suggests that these mutations may render breast cancer cells highly susceptible to replication stress failure caused by constitutively active CDK2. We initially uncovered these cell cycle responses through the use of CDK2 mutants that cannot be phosphorylated. However, we have now used pharmacologic inhibitors to induce CDK2-driven replication stress failure in breast cancer cell without intrinsic mutations that impact CDK2 phosphorylation, and we have established treatment regiments that specifically kill breast cancer cells but not untransformed mammary epithelial cells. If successful, this strategy will be rapidly translatable to clinical breast cancer applications, including the future development of a clinical trial.

RELEVANCE
The finding that mutations in genes that regulate the cell cycle are among the most common genetic changes in breast cancer cells led to the expectation that cell cycle-directed therapy would radically change therapy and outcomes. However, while this promise is now being realized with the use of CDK4/6 inhibitors in breast cancer therapy, CDK2, which mediates many oncogenic signaling pathways in breast cancer, has been more recalcitrant to this approach. Our work is focused to new ways to target CDK2 activity to enhance breast cancer therapy, through both p27 modulation, and through abnormal inhibitory phosphorylation. If successful, these approaches may be rapidly translated to new breast cancer treatment strategies..

The translational goal of this project is to evaluate the adoptive transfer of tumor-specific T cells derived or engineered from central memory cells to treat breast cancer. The immune system is designed to distinguish diseased from normal cells with exquisite specificity and sensitivity, and there is increasing evidence that tumor development and progression is restrained by adaptive host T cell responses to tumor-associated antigens. However, harnessing this activity to provide therapeutic benefit in breast cancer requires identifying antigens that are expressed by tumor cells and can be safely targeted, and developing methods to achieve potent and durable T cell immunity in patients. Many candidate tumor associated antigens have been discovered in breast cancer and we have focused on targeting the HER-2 oncoprotein and NY-BR-1. We have pursued the adoptive transfer of T cells specific for these antigens because this approach should allow for control of the specificity, function, and magnitude of the antitumor response, and could overcome obstacles that limit the endogenous host response, or T cell responses elicited by vaccination. The efficacy of adoptive T cell therapy in clinical trials for other human malignancies has been limited by the inability of tumor-specific effector cells that have been expanded in vitro to persist at high levels in vivo after adoptive transfer. Studies in our lab have demonstrated that the survival of adoptively transferred T cells is correlated with the differentiation state of the precursor T cell from which the T cells are derived. Effector cells isolated from central memory but not effector memory T cells provide persistent engraftment, migrate to memory T cell niches, function in vivo after adoptive transfer, and can be sustained at remarkably high levels by a short course of IL-15. This project will build on these findings and evaluate the adoptive transfer of T cells derived or engineered from central memory cells to treat breast cancer. The specific aims are: 1. To perform a phase I trial of adoptive T cell therapy with TCM-derived HER-2/neu (HER-2)-specific T cells following in vivo priming with a HER-2 peptide vaccine in patients with advanced HER-2+ breast cancer. 2. To engineer CD45RO+ CD62L+ TCM derived effector T cells through T cell receptor (TCR) gene transfer to express a TCR that targets NY-BR-1. 3. To perform a phase I study of adoptive T cell therapy with TCR modified TCM to target NY-BR-1 in patients with advanced NY-BR-1+ breast cancer.

RELEVANCE:
There is evidence breast cancer is detected by the immune system, but the development of immunotherapy that improves the outcome for patients has been challenging. The proposed studies will evaluate new approaches to the immunotherapy for breast cancer in which cells of the immune system that have the capacity to survive long term, will be isolated, programmed to target and kill tumor cells and transferred back to the patient. The results of these studies will provide insights into the potential utility of adoptive T cell therapy for breast cancer, and for the broader application of this approach in human malignancy.

The use of systemic chemotherapy for breast cancer has contributed to the recent decline in breast cancer mortality; however, an unacceptable number of patients fail systemic therapy and die of disseminated disease. Identifying factors important in resistance and directing patients towards more effective treatment is the translational goal of Project 3. Using quantitative PET imaging to measure glucose metabolism, and more recently dynamic contrast-enhanced (DCE) MRI to measure blood flow, we have identified an in vivo metabolic signature for locally advanced breast cancer (LABC) resistant to neoadjuvant chemotherapy as (1) a pre-therapy mismatch between metabolism and perfusion, (2) persistent or even increased tumor perfusion despite treatment, and (3) an altered pattern of glucose metabolism relative to glucose delivery after treatment. This pattern predicts incomplete response, early relapse and death independent of established prognostic factors, including pathologic primary tumor and nodal pathologic response. We have also found this pattern is more profoundly associated with triple-negative (TN, ER/PR/HER2 negative) tumors versus those that express ER/PR and/or over-express HER2.

We now propose to translate our clinical, in vivo findings in patients back into the laboratory to identify the biologic features of tumors underlying these findings. In a cohort of LABC patients undergoing neoadjuvant chemotherapy, we will (1) compare imaging findings to tumor phenotype determined by IHC and expression microarrays to determine which molecular pathways are most involved in the resistant imaging phenotype, (2) determine the role of the tumor microenvironment, specifically tumor hypoxia measured by FMISO PET and the expression of the hypoxic tissue markers measured by IHC, and (3) relate macroscopic metabolic properties measured by imaging to cellular metabolism in biopsy specimens and a panel of cell lines using ToF-SIMS, with the goal of relating findings on metabolic pathways measured in cell lines to the resistant phenotype seen in patients. Successful completion of the studies will identify breast cancer patients likely to fail systemic chemotherapy and direct therapy towards those biologic targets most likely to overcome resistance.

RELEVANCE:
This Project will investigate quantitative in vivo imaging as a means of identifying breast cancers resistant to systemic therapy and directing the patient towards more effective therapy. The primary translational goal of the project is to relate in vivo imaging findings predictive of poor response and patient outcome to underlying tumor biology with the goal of directing treatment targeted to specific resistance factors.

The three most common molecular subtypes of breast cancer, luminal A (40%), luminal B (30%), and basal-like (15%) vary considerably in their prognosis. A recent study with lengthy follow-up observed that the 10-year survival rate for women with luminal A tumors was 70%, but only 54% and 53% for women with luminal B and basal-like disease, respectively. (Kennecke JCO 2010;28:3271-7) Despite well-established differences in risks of recurrence and mortality, subtype specific prognostic factors remain largely unknown. Oncotype DX and MammaPrint testing have demonstrated the potential for molecular tumor characteristics to be clinically useful means of predicting risk of recurrence and guiding treatment decisions. However, at present Oncotype DX is only useful for women with hormone receptor-positive/HER2-negative breast cancers, which are primarily comprised of lower risk, less aggressive luminal A tumors; and MammaPrint is not specific to any particular molecular subtype of breast cancer. Thus, there is a clear clinical need for tools specifically tailored to identifying which patients with the more aggressive subtypes of breast cancer, luminal B and basal-like, have a high risk of recurrence and may benefit from more aggressive treatment and follow-up. There is also considerable value in identifying the substantial proportion of these patients who have a low risk of recurrence and could potentially avoid certain treatments.

Our research team is uniquely positioned to address this need. First, we have preliminary gene expression profiling data that demonstrates marked differences in the sets of molecular markers that are related to risk of recurrence in estrogen receptor (ER) positive vs. negative disease (unpublished data). Such differences are expected based on the underlying molecular heterogeneity across these two broadly defined groups of breast cancer. Second, we have extensive experience molecularly profiling breast tumors using formalin-fixed tissue specimens using a variety of platforms. Third, we have established substantial population-based resources needed for conducting this work with a robust sample size. Specifically, we have already enrolled more than 8,000 breast cancer patients into our various population-based studies and have subtyped approximately 2000 of them already into luminal A, luminal B, and basal-like groups.

Additionally, we have obtained detailed risk factor data and treatment information, as well as tumor tissue specimens, from these women. The size, depth of available information, and collection of biospecimens from this set of patients makes it uniquely suited for this type of work. Leveraging our expertise and resources we propose the following specific aims:

RELEVANCE:
The proposed project is innovative in that there are currently no tools for predicting prognosis among patients with luminal B and basal-like breast cancer. These patients have comparatively high risks of recurrence and poor survival rates. Both identifying those patients with poor outcomes who may warrant more aggressive care, as well as the substantial proportion of these patients who have very good outcomes and may require less intensive treatment and follow-up, has the potential to have near-term meaningful clinical impact.

Core A: Leadership

Core Co-Directors: Peggy L. Porter, MD
Martin (Mac) Cheever, MD

The Leadership Core provides the overall context for the translational activities of the SPORE and builds on established interdisciplinary collaborations. Dr. Porter and Dr. Cheever, Co-PIs of the SPORE, will co-direct the Core and lead an Executive Committee (EC), composed of all Project and Core leaders and breast cancer patient advocates, primarily responsible for overall planning and evaluation. The EC will be advised on scientific direction, planning and evaluation of the translational progress of SPORE projects and activities by both an External Advisory Board (EAB), which includes three national SPORE leaders, and an Internal Advisory Board (IAB), which include two SPORE leaders. To maintain a high degree of translational research focus to all SPORE activities, the EC will meet and interact regularly with the SPORE Career Development Program (CDP) and Developmental Research Program (DRP) committees, and the SPORE Statistical Working Group (SWG).

The aims of the Administrative Core are to:
1. Provide oversight of all SPORE activities to meet the scientific and administrative needs of the individual research projects and cores
2. In consultation with EAB members, integrate new projects into the SPORE
3. Provide an organizational structure within the FHCRC/UW Cancer Consortium (Consortium), which
a. promotes interaction between interdisciplinary investigators, in and outside of the SPORE
b. evaluates progress towards translational goals
c. encourages, selects and guides new research and developmental projects
d. provides career mentorship and entry of women and minorities into the field of breast cancer research
4. Promote SPORE-SPORE interactions, within and outside the Consortium
5. Provide fiscal management of grant funds and records in compliance with all regulations and requirements, including Radiation Safety, Animal Care, and Protection of Human Subjects
6. Communicate and consult with NCI project officers

CORE B: Specimen Acquisition and Pathology

Core Director: Peggy Porter, MD

Co-investigator: Ming-Gang Lin, MD

The Specimen Acquisition and Pathology Core is a key component of the SPORE and will support the translational goals of SPORE Projects, as well as developmental projects funded through the SPORE. Dr.
Porter’s leadership will provide not only research and clinical breast pathology expertise but also integration of Core B activities with the SPORE overall, and developmental projects in particular. This coordination of specimen acquisition and distribution with promotion of new research will greatly aid translation of basic discoveries into experiments involving human samples. The Core augments the existing robust FHCRC/UW Cancer Consortium Breast Specimen Repository and Registry (BSRR) and will function to centralize specimen acquisition, processing, pathologic analysis and distribution of samples needed by SPORE projects. It will also provide a laboratory base for select biomarker assays in support of the major and developmental projects.

Specifically the Core will:
1. Use the established and efficient BSRR to procure and distribute tissue and blood specimens for
2. SPORE and developmental projects
3. Perform protocol-specific specimen processing for SPORE and developmental projects
4. Maintain a database that allows specimen tracking and distribution, linkage with relevant deidentified data, and data sharing with other projects and cores
5. Provide high-quality pathology support for SPORE and developmental projects including:
• Pathology review of tissues at various levels of complexity
• Histology sectioning and preparation of section slides for histologic evaluation
• Immunohistochemistry (IHC), and new antibody work-up and optimization
• IHC interpretation of both immunoperoxidase and immunofluorescence stains
• Laser capture microdissection (LCM)
• Tissue microarray (TMA) design, construction, sectioning, and imaging

RELEVANCE:
The Specimen Acquisition and Pathology Core is a key component of the SPORE and will support the translational goals of the projects and developmental projects. The core will take full advantage of institutional resources, integrate them for efficient use by SPORE investigators, and flexibly adapt to needs and new developmental projects during the time frame of the SPORE grant.

CORE C: Clinical

Core Director: Julie Gralow, MD

Co-investigators: Vijayakrishna K. Gadi, MD, PhD
Jennifer Specht, MD

For translational research to be successful there must be a two-way flow of information, from the clinic to the laboratory and from laboratory to clinic. Clinical interaction with patients and health care providers is crucial to the success of the research studies proposed within the SPORE, and to the long-term success of a translational program of breast cancer research. The Clinical Core of the SPORE program provides this critical link by incorporating a highly-effective breast cancer clinical team into the overall structure of the SPORE. The Clinical Core will be responsible for facilitating translational research through the support of clinical trials and clinical research studies, as well as providing clinical education throughout the program. Additionally, the Clinical Core will serve to mentor and find clinical collaborators for laboratory investigators, with particular emphasis on those funded through the SPORE’s Developmental Research Program.

The Clinical Core will assist SPORE investigators interested in initiating a clinical study, including preparation, review, approval, and activation of clinical studies. Interactions with patients and health care providers will be initiated and facilitated by the Clinical Core. The Core research manager will supervise research staff who will assist with SPORE-related clinical trials to ensure that accrual is achieved, overseeing clinical trials recruitment efforts, screening for trial eligibility, and contacting potential patients regarding study participation. The Core will communicate with institutional and regional oncology providers to seek physician support for referral into SPORE projects. The Core will consent and follow-up patients appropriate for SPORE projects and provide clinical and outcome data as required by these studies. The Clinical Core staff will be responsible for assuring that the clinical protocol is safely and properly followed, including monitoring toxicities and reporting adverse events. They will provide support and education to participating patients, assist in the administration of therapy, and assure timely entry of clinical data. By design, the Clinical Core will work closely with the Specimen Acquisition and Pathology Core, which will procure and process specimens for SPORE projects after initial contact is made through the Clinical Core. The Clinical Core will interact closely with the Biostatistical Core in designing and analyzing studies, and will be in close interface with the FHCRC/UW Consortium’s Clinical Trials Support Office that is responsible for management of all clinical trials.

RELEVANCE:
The importance of clinical expertise to effectively carry out translational research objectives cannot be overstated. Laboratory discoveries can only be developed into clinical tools if clinical input is incorporated early into all aspects of research planning and implementation. This Core is well-positioned to take advantage of FHCRC/UW Consortium research, clinical strengths and institutional alliances to maximize exchange of ideas and facilitate translation, both to and from the clinic.

CORE D: Biostatistics

Core Director: Li Hsu, PhD

Co-investigators: Ted Gooley, PhD
Barry Storer, PhD
Pei Wang, PhD

The Biostatistics Core will provide essential biostatistical support to Seattle Cancer Consortium Breast
SPORE investigators. The Core links study design, data collection, measurements, and analysis to the critical hypotheses and questions studied by SPORE investigators whose research involves basic sciences, epidemiology, population studies, and clinical research. The Biostatistics Core will contribute to the SPORE mission through the following specific aims:
1. Study design: Define study hypotheses, study populations, and experimental measurements to answer research questions of interest, avoid systematic bias, and ensure a high likelihood of detection of biologically meaningful effects.
2. Analysis and interpretation: Identify and implement appropriate quantitative methods to address scientific questions of interest and provide valid statistical inferences about the evidence supporting the various study hypotheses.
3. Methodological development when needed: Modify existing approaches and develop novel study designs and methods to address problems arising from SPORE projects, where appropriate statistical methods are inadequate.

SPORE biostatisticians have been closely involved with the projects in the SPORE. They will continue to collaborate as co-investigators on each project to ensure that studies are well designed and appropriately analyzed and interpreted. Moreover, the Core will provide consulting services to SPORE investigators for projects under the Research Developmental Program and the Career Development Program. The Core investigators have diverse and complementary expertise, and can conduct analyses using data from a wide variety of experimental technologies. For some of these technologies, analytic methods are still evolving. Core investigators are part of Consortium biostatistical research groups that are leaders in the areas of biomarker development, computational biology, and bioinformatics. In summary, the Core is well equipped to meet the diverse needs and address the translational aims of the Breast SPORE.

RELEVANCE:
This new Core will provide essential statistical support and analysis to current and future SPORE projects.

Developmental Research Program

Director: Peggy L. Porter, MD

The goal of the Developmental Research Program (DRP) in the Seattle Cancer Consortium (SCC) Breast
SPORE is to identify, fund and nurture innovative projects that have the potential to become outstanding translational research efforts. This will ensure that mature projects are in the pipeline when current projects meet their translational goals or when SPORE Projects fail to meet their aims and need to be replaced. Additionally, it will ensure that mature projects are ready for the competing renewal application towards the end of the grant period.

The members of the SPORE realize that real research progress requires that all aspects of prevention, detection, diagnosis, treatment and survivorship be addressed. This necessitates a DRP committee with diverse representation that works to attract candidates and developmental projects spanning all research and clinical disciplines. The aims of the DRP are to:
1. Stimulate research efforts that include multidisciplinary interactions with clinical and basic scientists inside and out of the participating institutions, including inter-SPORE interactions
2. Provide 1-2 years of developmental project funding for the most innovative investigator-initiated projects in all areas of translational breast cancer research
3. Target funds to specific areas that are especially likely to advance the translational research goals of the SCC Breast SPORE
4. Monitor developmental projects so that one or more are in a position to replace full projects that either complete their aims or are not progressing satisfactorily

Career Development Program

Director: Martin (Mac) Cheever, MD

Goals of the Seattle Cancer Consortium (SCC) Breast SPORE Career Development Program (CDP) are as
follows:
1. Provide research support for advanced fellows, junior faculty and established investigators who wish to develop or refocus their careers on translational breast cancer research
2. Provide a system for mentoring faculty pursuing breast cancer research in a broad range of disciplines
3. Create a framework in which investigators can gain exposure to, and possibly training in, aspects of translational breast cancer research outside their areas of expertise (e.g., a molecular biologist would be exposed to clinical issues in breast cancer care by attending tumor boards and clinical breast cancer conferences)
4. Provide a mechanism by which innovative ideas can develop into promising translational studies in breast cancer research
5. Help attract and retain women, minorities and developing faculty who can make key contributions to translational breast cancer research at the Fred Hutch (FHCRC) and University of Washington (UW)
6. Create a synergistic environment for translational breast cancer research with other SPORE programs nationwide